removed when we last updated the volume. It's actually
still available on disk, though, and can be re-enabled in your
tool_conf.xml by adding the following back to your Get Data section:
tool file=data_source/ebi_sra.xml /
-Dannon
On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian
Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205
On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker dannon.ba...@gmail.com wrote:
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote:
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the
next
Hi Cloudman Development Team,
I noticed on the most recent Cloudman release (revision
11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a)
that there is no option to Get Data from the ENA SRA. We've found that
retrieving large (fastq) data sets from public databases
:
Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian:
Hi Bjorn,
Thanks for the quick response.
I am running version: 10201:ebe87051fadf, when I updated to the latest
version, I was able to start the install of DeepTools. The tool
seemed to be installing but when I went
Hello,
I recently discovered the DeepTools program and have been looking forward
to using it with Galaxy Cloudman. Today I attempted to load DeepTools from
the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and
got the following error:
Internal Server ErrorGalaxy was unable to
Hi Bjorn,
Thanks for the quick response.
I am running version: 10201:ebe87051fadf, when I updated to the latest
version, I was able to start the install of DeepTools. The tool seemed to
be installing but when I went to refresh the page, I was greeted with this
message: Initializing repository
Hello,
I found a couple of issues in using the latest version of Cloudman
(revision:10201:ebe87051fadf).
The Extract Genomic DNA tool returns an error:
No sequences are available for 'mm9', request them by reporting this
error.
Upon trying to report the error in Galaxy (on the page that comes up
:
On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote:
Hi,
I am having trouble setting up a FTP connection with the recently
released version of Galaxy Cloudman (ami-118bfc78).
I have instantiated the new version of Galaxy Cloudman with CloudLaunch
and also through the AWS EC2 wizard
Cufflinks, Cuffcompare, and Cuffdiff are also failing to run because they
can not be found. I am using the newly released version of Cloudman 2.0 (
ami-118bfc78).
Any help would be appreciated.
Cheers,
Mo Heydarian
On Mon, Jul 8, 2013 at 5:02 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote:
Hi,
I am having trouble setting up a FTP connection with the recently released
version of Galaxy Cloudman (ami-118bfc78).
I have instantiated the new version of Galaxy Cloudman with
CloudLaunchhttp://usegalaxy.org/cloudlaunch and
also through the AWS EC2 wizard (using the same security group
Hi,
Is there a way to export visualizations from Trackster and Sweepster in
.pdf or .jpg format? I have been using these fantastic tools to fine tune
my parameters and would like to show how I did so in figure format
(partially to locally get the word out about these powerful tools).
Screenshots
instance.
Try using the admin console to update to the most recent Galaxy dist using
this URL:
https://bitbucket.org/galaxy/galaxy-dist/
(not galaxy-central, as is the default)
Best,
J.
On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote:
We are running galaxy-cloudman-2011-03-22 (ami
We are still getting empty TopHat output files on our Galaxy instance on
the cloud. We see that TopHat is generating data while the tool is running
(by monitoring our disk usage on the Amazon cloud), but the output is
empty files.
Is anyone else having this issue? Does anyone have any
We have been having also been having this issue, we get empty TopHat output
files. This is happening on two instances that were started within the past
three weeks on the cloud.
Cheers,
Mo Heydarian
-- Forwarded message --
From: 吳正華 joh...@ibms.sinica.edu.tw
Date: Fri, Oct
Hello,
I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I
have since not been able to run any jobs. I get the following error:
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'blastxml': 'module' object has no attribute 'BlastXml'
Hi Galaxy Community!
Hope all is well.
I've been trying to install some tools in my Galaxy Cloudman instance
(using image: ami-da58aab3 ) from the main toolshed. When I try to
install to local Galaxy I get the error:
Not Found
The resource could not be found.
No action for
Hi,
I have been trying to use trackster on the main Galaxy server for a couple
of days now. It was working fine for me early yesterday, I was looking at
(larger) BAM files, then it just stopped and would not display the data of
the loaded tracks (but did display the track title). I have tried to
Hello,
I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf
files just fine, but not the merged transcripts.gtf file from Cuffmerge.
This is the first time this has happened.
After I upload my merged transcripts.gtf file (via ftp) I can not move
the file to the history pane.
Heydarian
PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
414 Hunterian
Baltimore, MD 21205
On Thu, May 3, 2012 at 8:19 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote:
Hello,
I can not upload Cuffmerge files to Galaxy Cloudman. I can load
Hello,
I am performing NGS data analysis using Galaxy cloudman. I am working with
very large Fastq files that add up and approach the 1TB limit of the EBS
volume when I perform my analysis. Is there a way to use multiple EBS
volumes with one EC2 instance of Galaxy cloudman. For example, could I
Hello,
I am trying to connect an EC2 instance to an EBS volume.
I have attached the EBS volume to the EC2 instance (running Galaxy). I now
need to mount the EBS volume to the EC2 instance. To do this I will use
Putty to make the connection. But first I have to convert the private key
from .pem
Hello,
I am new to cloud computing and am trying to use the Galaxy cloudman
service through Amazon to analyse NGS data. I have a couple of questions
regarding data transfer:
If I am running an EC2 instance, with an EBS volume attached, how can I
retrieve the data from the EBS volume? In addition,
Hello,
How do you connect existing EBS volumes to a fresh EC2 instance on Amazon?
I have been starting the EC2 instance and choosing test cluster where the
option to use EBS volume space is given (when the Galaxy cloud console
starts up), since there is no place to insert my EBS volume address.
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